Current Dev State

static/js/ketcher2/script/ui/structformat.js

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+/****************************************************************************
+ * Copyright 2017 EPAM Systems
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ***************************************************************************/
+
+import molfile from '../chem/molfile';
+
+export const map = {
+	'mol': {
+		name: 'MDL Molfile',
+		mime: 'chemical/x-mdl-molfile',
+		ext: ['.mol'],
+		supportsCoords: true
+	},
+	'rxn': {
+		name: 'MDL Rxnfile',
+		mime:'chemical/x-mdl-rxnfile',
+		ext: ['.rxn'],
+		supportsCoords: true
+	},
+	'cml': {
+		name: 'CML',
+		mime: 'chemical/x-cml',
+		ext: ['.cml', '.mrv'],
+		supportsCoords: true
+	},
+	'smiles': {
+		name: 'Daylight SMILES',
+		mime: 'chemical/x-daylight-smiles',
+		ext: ['.smi', '.smiles']
+	},
+	'smarts': {
+		name: 'Daylight SMARTS',
+		mime: 'chemical/x-daylight-smarts',
+		ext: ['.smarts']
+	},
+	'inchi': {
+		name: 'InChI String',
+		mime: 'chemical/x-inchi',
+		ext: ['.inchi']
+	}
+};
+
+export function guess (structStr, strict) {
+	// Mimic Indigo/molecule_auto_loader.cpp as much as possible
+	const molStr = structStr.trim();
+
+	if (molStr.indexOf('$RXN') !== -1)
+		return 'rxn';
+
+	const molMatch = molStr.match(/^(M  END|\$END MOL)$/m);
+
+	if (molMatch) {
+		const end = molMatch.index + molMatch[0].length;
+		if (end === molStr.length ||
+			molStr.slice(end, end + 20).search(/^\$(MOL|END CTAB)$/m) !== -1)
+			return 'mol';
+	}
+	if (molStr[0] === '<' && molStr.indexOf('<molecule') !== -1)
+		return 'cml';
+
+	if (molStr.slice(0, 5) === 'InChI')
+		return 'inchi';
+
+	if (molStr.indexOf('\n') === -1) // TODO: smiles regexp
+		return 'smiles';
+
+	// Molfile by default as Indigo does
+	return strict ? null : 'mol';
+}
+
+export function toString (struct, format, server, serverOpts) {
+	console.assert(map[format], 'No such format');
+
+	return new Promise((resolve, reject) => {
+		var moldata = molfile.stringify(struct);
+		if (format === 'mol' || format === 'rxn')
+			resolve(moldata);
+		else
+			resolve(server.then(() => (
+				server.convert({
+					struct: moldata,
+					output_format: map[format].mime
+				}, serverOpts)
+			), () => {
+				throw Error(map[format].name + ' is not supported in the standalone mode');
+			}).then(res => res.struct));
+	});
+}
+
+export function fromString (structStr, opts, server, serverOpts) {
+	return new Promise(function (resolve, reject) {
+		const format = guess(structStr);
+		console.assert(map[format], 'No such format');
+
+		if (format === 'mol' || format === 'rxn') {
+			const struct = molfile.parse(structStr, opts);
+			resolve(struct);
+		} else {
+			let withCoords = map[format].supportsCoords;
+			resolve(server.then(() => (
+				withCoords ? server.convert({
+					struct: structStr,
+					output_format: map['mol'].mime
+				}, serverOpts) : server.layout({
+					struct: structStr.trim(),
+					output_format: map['mol'].mime
+				}, serverOpts)
+			), () => {
+				throw Error(map[format].name + ' is not supported in the standalone mode');
+			}).then(res => {
+				let struct = molfile.parse(res.struct);
+				if (!withCoords)
+					struct.rescale();
+				return struct;
+			}));
+		}
+	});
+}
+
+// Pretty stupid Inchi check (extract from save)
+export function couldBeSaved(struct, format) {
+	if (format === 'inchi') {
+		if (struct.rgroups.count() !== 0)
+			throw 'R-group fragments are not supported and will be discarded';
+		struct = struct.clone(); // need this: .getScaffold()
+		struct.sgroups.each((sgid, sg) => {
+			// ? Not sure we should check it client side
+			if (sg.type !== 'MUL' && !/^INDIGO_.+_DESC$/i.test(sg.data.fieldName))
+				throw Error('InChi data format doesn\'t support s-groups');
+		});
+	}
+}